I disagree, but would qualify that. In the Biologic sciences I would argue that the best tool is Word with the Endnote or Reference Manager plug in. It auto-formats your references according to the journal you submit to.
There is also the cost, if he migrates this way, of that a lot of people, me included, who would go- yah sure dude whatever.... and just ignore him. 2 people give me equall things to do, 1 of which is easy.... the other person is probably out of luck.
I use Ella from OpenField Software. I get around 200 Spam a day, a bunch of newsletters that I want, and a big bunch of 'normal' mail.
I have had it for about 2 weeks. In the last 3 days I have had 2 false +'s (messge in Spam that shouldn't be there) and 4 that went to the newsletter folder that shouldn't have.
Nope - Not Perl. C++ and Java. Perl won't get it done. Data set sizes are too large and speed too important. Crap code won't sell either (as that feature does shine through), and we are distinctly a 'for profit' entity.
I would agree that the best stuff comes out of a tight collaboration between developers and Biologists, but both parties involved need to know the others language. We have seen many of the folks coming out the Bioinformatics programs that are just CS people who thought there was money to be made in Bioinformatics... This way lies darkness. If they don't understand the Biology, and for the most part the Bioinformatics people we have dealt with don't, then they are not as much use as someone who understands both. People who are interested in code frequently get stuck in the "because it is cool" or "Because I can" type of development, in stead of stepping back and wondering "Why would you do that" or "Does that tell me anything?"
I work for a Bioinformatics company. Biology Biology Biology Biology!!! We have, and they are not doing as well, several people who with more of a CS background. They don't understand what it is that they are writing programs/algorithms about. We have found it easier to take Biologists who know computers and get good work from them than to do the converse. Make sure you get a VERY good grounding in basic biology. If you don't know what the data you are looking at mean, in the biological sense, then you will make the same mistake a lot do. Just because an algorithm is cool doesn't mean it makes sense. Only by understanding the Biology can you understand the difference.
As someone who speaks to the press, albeit in a different field, it is also the responsibility of the person being interviewed to MAKE SURE the reporter gets it. If they don't ask good questions, make sure you give them the answers to the questions they didn't know to ask. You have to assume that they are unfamiliar with the area they are writing about and thus try and educate tehm. Yes, that smacks of doing their job for them, but you have to help them do this. Fair? probably not. Reality? Yep.
I must be missing something. Having just completed a Ph.D. in Immunology, there was nothing surprising about the genome map. Alternative splicing has been known for awhile (at least 10 years, probably longer but I am lazy and don't want an exact date right now), which is essentially what they are all talking about. Gene therapy will work just as well in this environment as any other, as the problem of fixing a single defect remains the same. The problems with gene therapy right now are delivery and targeting. Once those are solved (IF those are solved) then whether it was one gene=one protein or not doesn't matter. You fix the point mutation and get on down the road. Don't change the sequence surrounding it, and you don't have a problem.
The article is misleading as well in regards to what affymatrix and others sell. They sell clones dervived from mRNA, which is just as valuable whether it came from alternative splicing or from individual genes. You just adjust your thinking, but your data remains true and valuable. Proteins come from mRNA, and then can also be modified for another level of control, so you know you aren't at the end of the story, but you do have to start somewhere.
The control of splicing will involve control proteins, that will be made by mRNA, that will be turned on and off by other control proteins...etc... going backwards in an endless loop of feedback loops.
This is why the field of Bioinformatics is taking off. You can't hold it all in your head, even for a simple pathway.
Well, I think that you have insanely high standards for what counts as innovative, then. To suggest that the genome was just applied engineering ignores the tremendous developments in informatics that were necessary to make it possible. More importantly, the way that genomic data is used is qualitatively different from the way that genetic data was used before the concept of genomics. Furthermore, the genome is really only the leading edge of future biology; proteomics didn't even exist 10 years ago, and it depends absolutely on genomic data.
True- but is was not surprising it was going to get done. It has been talked about, and been a goal since DNA sequencing was found. I guess I count it as engineering not innovation becuase no one was surprised that it got finished. There were (as we both mentioned) a lot of little steps along the way that in and of themselves are not that important, but overall massivly speeded up the final output (bioinformatics as an entire field). The fact that 2 groups were serious contenders, and that there were people all over the world contributing, and that in the end I think Celera won because they bought the faster more expensive machine and a different strategy make it more of an engineering feat than an innovation. Guess it is a matter of semantics, but I would say the bioinformatics advances were innovative, but the sequencing wasn't.
I think this discussion points to the nature of the way science moves. Innovation rarely looks like innovation when it is being done, it is only later that anyone noticies (lag time to acceptance) and would say that revolutionary ideas in science behave a bit the same way (is there a difference between revolutionary scientific ideas and innovation????)...with slow grudging acceptance.
You should read the biology literature more closely. The statement "Innovation of every page" is laughable. In every field, there is good and bad research. It does not follow More Journals --> more innovation and more than it follows more published articles --> smarter person. It may hold true that more GOOD articles --> smarter person. One really good published article should beat 5 really crappy ones.
I was unaware that apple was trying to get the FSF's approval. Further, you don't hear the BSD people complaining about apple, you mostly hear praise. I would think that just agreeing with the BSD camp (and their FSF unacceptable liscence) would probably torpedo apple regardless of what they do.
It seemed to me that advertisers noticed as well, as I could have sworn there were more (and differant) ad's last night than there were on sunday night.
My wife didn't like it that much, because she hadn't read Dune. I think there could have been more background for those unfamiliar with what was going on. Overall I thought it rocked, with only minor annoyance at some of the cheesy background effects (some looked REALLY fake)
Said Congress might eventually revisit the DMCA: "Judges are not best suited to deal with cases like these. Judges are best suited to deal with matters between private parties.... Judges do not have any special training to rule on decisions such as these and lack the objective perspective to make those best decisions."
on the second page..... for those who read past the first paragraph. I think this judge is a little more level headed than he is being given credit for. In another quote he says the internet is the fourth great age of communication (starts with writing).
I am being paid poorly to be a propaganda machine, and I am pissed.
For a good example of no government involvement in the economy, look at somalia. There you have business arguing the exact oppisate that you are. They have no infrastructure (roads, telephones, water etc...) and they don't like it.
I don't beleive that there is any data that the economy (will/will not) stop working if patents were abolished. I do however think, that with the current way that things work, abolishing patents in the life sciences field would stop work on derivative medicines. I base this judgement on knowing how much it costs to get the work done, and how much of the time trials fail, and how long it takes before failure. If you were to remove protection from those companies, I would found a company tomarrow to ONLY make medicines that I knew were profitable.
Where would the inducement be to do research? You are not going to be able to recoup any of the money that you spend on the research, so why spend it? Competitors will just see what you have done, copy it, and the price will fall to exactly what it costs to produce the drug + whatever the market will bear. There is no room there to pay the people (100's) who spent decades (10 years at a minimum) sheperding it through clinical trials (and thus insuring that we don't kill people). You have to be able to recoup costs, and the governement is the only group that can make sure you do.
Several Things:
I think patents, in this case, are a good thing. For example, Genentech patented EPO, and on the basis of this patent produced drugs (recombinant EPO). The time line for drug production, clinical trials, etc... is around 10-15 years, with a price tage or many millions. WHY, without protection from other people piggybacking on your work, would you do this? It is fine to claim that people are blindly patenting, but from a personal perspective of actually being one of those evil people, I think that this is an incorrect statement. We, and everyone else that does this DOES HAVE SOME IDEA. Does that mean that we have all the answers? NO, but to get those answers takes years and dollars, and not insignificant numbers of either of them. Without patent protection, drug companies will not get within a million miles of the gene. All that can be produced with non-patented genes are generic drugs, on which drug companies do not make money. You can argue they make too much money, but there is a reason that the US is at the forefront of the medical world, and money is a pretty good explanation. I do beleive selfish motivation produces the drugs, as that produces the money, and gets you the recognition. This is not like a software problem, where it will be solved by next year. Each gene WILL take years and millions of $, and with a failure rate (defined as not usefull for making a drug out of) at around 80%, you need some protection for the ones that work or you will never make any money.
EST patents are still under question, with no defense of them being mounted, but I would agree that they suck. You have no function on them at all, so patents on them are wrong. For whole genes, function is a lot more clear (although real far from crystal clear).
On a related note: If you get govenment grants (majority of researchers in US) you are required to patent, or otherwise protect your work BY LAW. Failure to do so will get you, and your university, in trouble.
I would guess that Larry Elison will not fight this. As everyone else has mentioned, most of the larger database companies have this provision in their EULA, Oracle being no exception. If Larry fights and wins, well he hasn't done his company any big favors, as now he will have also invalidated his own companies ban as well. I would guess he would be quiet now, as he has made his point, the press has noticed, and he doesn't have to say anything more to keep this story alive. The last thing he probably wants is to have that clause of EULA's tested.
Then again, IANAL and maybe Larry Elison doesn't care.
Pretending that politics are dead is a bit like the situation with the legal system and the online world. Online world pretends 100's of years of legal system will evaportate, and is then very shocked when it doesn't. Yes, most people who are not lawyers don't understand it, but that doesn't make it irrelevant. My uncle is a judge, and when he hears the cry's that the legal system is dead or that it can't keep up with the online world, He laughs and makes a comment about foolish young people who will grow up and learn. I think the same is true of politics. I think humans are political. You may be disgusted with the current system, but you can't pretend it doesn't matter (you do drive on roads, use libraries, call the police/fire dept etc... for which government is CRITICAL). Further, I think that government and politics are in-seperable. The second you have a concentration of power is the same second that you will have people fighting for it ( I think power is neccesary to get anything done, for and example of this not working, look at Somalia right now- massive lack of regualtion, and many there want a govenment so they can get infrastructure).
I think the utopian veiw has always existed just 30 years out, and that it will always remain about that far away. Humans will probably always be human (barring massive genome changes)
They announced that it will ship in the beginning of next year, and that the beta would be late summer this year. So far they have hit the beta release date (it was LATE summer!) but they haven't had a chance to miss the final release date yet. I give them an odds on chance of hitting it, but we will see.
I don't neccesarily think this is so. More people would give your more editing, more oversite to make sure one person is not writing garbage, more orginization, and more mouths to feed. Many will say that linux documentation works this way, I would disagree. Consistent style and presentation goes a long way toward making the book usefull, understandable, and ultimatly marketable. More cooks spoil the brew (in writing, not Coding, although I could argue that is true as well).
I can''t speak for your school, but at mine we do not own the work. The school does (PhD) thesis. I am in the process of writing as we speak (should not be reading this) and have to sighn the copyright assighnment sheet to turn the thesis into the library. It is similar to when we publish papers in refereed journals, we also lose that copyright.
I am in biology (molecular immunology), so your field/school may be differant (sounds like it is) but I would not say the blanket statement that all of these thesis's (?thesi?) are taken without permission.
The other serious mistake the author makes is somehow equating Linux as a GUI, then the GUI is xfree86. Ironically, X Windows is one of the oldest GUI's in existance, and the author is trying to make the point that it is too "new" to be mature and compete.
I remain uncertain as to the link between age-consistancy-quality-and ease of use. He says nothing about it being too new. Gnome and KDE are too new. They are still playing catch up to windows and the Mac.
And yet it's one of the most popular OSS programs today. Not a very good example of OSS failing is it?
By this criteria Windows is the best program in the world, and Microsoft writes all the best software in the world.
This truely is misleading, anyone can take a project and branch off of it is they feel the maintainer is not doing a good job
True- please start distributing your Linux Kernal with all the modifications that Linus et al do not want. The good projects HAVE not had this done to them, and there does seem to be an overlap been a group controlling and quality software (kernal, apache)
Slashdot Mirror
I disagree, but would qualify that. In the Biologic sciences I would argue that the best tool is Word with the Endnote or Reference Manager plug in. It auto-formats your references according to the journal you submit to.
There is also the cost, if he migrates this way, of that a lot of people, me included, who would go- yah sure dude whatever.... and just ignore him. 2 people give me equall things to do, 1 of which is easy.... the other person is probably out of luck.
I use Ella from OpenField Software. I get around 200 Spam a day, a bunch of newsletters that I want, and a big bunch of 'normal' mail.
I have had it for about 2 weeks. In the last 3 days I have had 2 false +'s (messge in Spam that shouldn't be there) and 4 that went to the newsletter folder that shouldn't have.
Nope - Not Perl. C++ and Java. Perl won't get it done. Data set sizes are too large and speed too important. Crap code won't sell either (as that feature does shine through), and we are distinctly a 'for profit' entity.
I would agree that the best stuff comes out of a tight collaboration between developers and Biologists, but both parties involved need to know the others language. We have seen many of the folks coming out the Bioinformatics programs that are just CS people who thought there was money to be made in Bioinformatics... This way lies darkness. If they don't understand the Biology, and for the most part the Bioinformatics people we have dealt with don't, then they are not as much use as someone who understands both. People who are interested in code frequently get stuck in the "because it is cool" or "Because I can" type of development, in stead of stepping back and wondering "Why would you do that" or "Does that tell me anything?"
I agree though- you need both.
I work for a Bioinformatics company. Biology Biology Biology Biology!!! We have, and they are not doing as well, several people who with more of a CS background. They don't understand what it is that they are writing programs/algorithms about. We have found it easier to take Biologists who know computers and get good work from them than to do the converse. Make sure you get a VERY good grounding in basic biology. If you don't know what the data you are looking at mean, in the biological sense, then you will make the same mistake a lot do. Just because an algorithm is cool doesn't mean it makes sense. Only by understanding the Biology can you understand the difference.
As someone who speaks to the press, albeit in a different field, it is also the responsibility of the person being interviewed to MAKE SURE the reporter gets it. If they don't ask good questions, make sure you give them the answers to the questions they didn't know to ask. You have to assume that they are unfamiliar with the area they are writing about and thus try and educate tehm. Yes, that smacks of doing their job for them, but you have to help them do this. Fair? probably not. Reality? Yep.
I don't think Google has proven anything of the sort.
Have they made money yet?
Until they do, they aren't a success in the sense that they will be around for a long time. Just being good isn't enough. You also have to make money.
I must be missing something. Having just completed a Ph.D. in Immunology, there was nothing surprising about the genome map. Alternative splicing has been known for awhile (at least 10 years, probably longer but I am lazy and don't want an exact date right now), which is essentially what they are all talking about. Gene therapy will work just as well in this environment as any other, as the problem of fixing a single defect remains the same. The problems with gene therapy right now are delivery and targeting. Once those are solved (IF those are solved) then whether it was one gene=one protein or not doesn't matter. You fix the point mutation and get on down the road. Don't change the sequence surrounding it, and you don't have a problem.
The article is misleading as well in regards to what affymatrix and others sell. They sell clones dervived from mRNA, which is just as valuable whether it came from alternative splicing or from individual genes. You just adjust your thinking, but your data remains true and valuable. Proteins come from mRNA, and then can also be modified for another level of control, so you know you aren't at the end of the story, but you do have to start somewhere.
The control of splicing will involve control proteins, that will be made by mRNA, that will be turned on and off by other control proteins...etc... going backwards in an endless loop of feedback loops.
This is why the field of Bioinformatics is taking off. You can't hold it all in your head, even for a simple pathway.
Well, I think that you have insanely high standards for what counts as innovative, then. To suggest that the genome was just applied engineering ignores the tremendous developments in informatics that were necessary to make it possible. More importantly, the way that genomic data is used is qualitatively different from the way that genetic data was used before the concept of genomics. Furthermore, the genome is really only the leading edge of future biology; proteomics didn't even exist 10 years ago, and it depends absolutely on genomic data.
True- but is was not surprising it was going to get done. It has been talked about, and been a goal since DNA sequencing was found. I guess I count it as engineering not innovation becuase no one was surprised that it got finished. There were (as we both mentioned) a lot of little steps along the way that in and of themselves are not that important, but overall massivly speeded up the final output (bioinformatics as an entire field). The fact that 2 groups were serious contenders, and that there were people all over the world contributing, and that in the end I think Celera won because they bought the faster more expensive machine and a different strategy make it more of an engineering feat than an innovation. Guess it is a matter of semantics, but I would say the bioinformatics advances were innovative, but the sequencing wasn't.
I think this discussion points to the nature of the way science moves. Innovation rarely looks like innovation when it is being done, it is only later that anyone noticies (lag time to acceptance) and would say that revolutionary ideas in science behave a bit the same way (is there a difference between revolutionary scientific ideas and innovation????)...with slow grudging acceptance.
You should read the biology literature more closely. The statement "Innovation of every page" is laughable. In every field, there is good and bad research. It does not follow More Journals --> more innovation and more than it follows more published articles --> smarter person. It may hold true that more GOOD articles --> smarter person. One really good published article should beat 5 really crappy ones.
I was unaware that apple was trying to get the FSF's approval. Further, you don't hear the BSD people complaining about apple, you mostly hear praise. I would think that just agreeing with the BSD camp (and their FSF unacceptable liscence) would probably torpedo apple regardless of what they do.
It seemed to me that advertisers noticed as well, as I could have sworn there were more (and differant) ad's last night than there were on sunday night.
My wife didn't like it that much, because she hadn't read Dune. I think there could have been more background for those unfamiliar with what was going on. Overall I thought it rocked, with only minor annoyance at some of the cheesy background effects (some looked REALLY fake)
Said Congress might eventually revisit the DMCA: "Judges are not best suited to deal with cases like these. Judges are best suited to deal with matters between private parties.... Judges do not have any special training to rule on decisions such as these and lack the objective perspective to make those best decisions."
on the second page..... for those who read past the first paragraph. I think this judge is a little more level headed than he is being given credit for. In another quote he says the internet is the fourth great age of communication (starts with writing).
I am being paid poorly to be a propaganda machine, and I am pissed.
For a good example of no government involvement in the economy, look at somalia. There you have business arguing the exact oppisate that you are. They have no infrastructure (roads, telephones, water etc...) and they don't like it.
I don't beleive that there is any data that the economy (will/will not) stop working if patents were abolished. I do however think, that with the current way that things work, abolishing patents in the life sciences field would stop work on derivative medicines. I base this judgement on knowing how much it costs to get the work done, and how much of the time trials fail, and how long it takes before failure. If you were to remove protection from those companies, I would found a company tomarrow to ONLY make medicines that I knew were profitable.
Where would the inducement be to do research? You are not going to be able to recoup any of the money that you spend on the research, so why spend it? Competitors will just see what you have done, copy it, and the price will fall to exactly what it costs to produce the drug + whatever the market will bear. There is no room there to pay the people (100's) who spent decades (10 years at a minimum) sheperding it through clinical trials (and thus insuring that we don't kill people). You have to be able to recoup costs, and the governement is the only group that can make sure you do.
DNA is opensource. The genome is mostly online and searchable. Develop the technology and you will be able to apply diffs.
Yes- OOOOOOPPPPs
Genentech was the growth hormone I think (must drink more coffee) but as you say it doesn't make much difference
Several Things:
I think patents, in this case, are a good thing. For example, Genentech patented EPO, and on the basis of this patent produced drugs (recombinant EPO). The time line for drug production, clinical trials, etc... is around 10-15 years, with a price tage or many millions. WHY, without protection from other people piggybacking on your work, would you do this? It is fine to claim that people are blindly patenting, but from a personal perspective of actually being one of those evil people, I think that this is an incorrect statement. We, and everyone else that does this DOES HAVE SOME IDEA. Does that mean that we have all the answers? NO, but to get those answers takes years and dollars, and not insignificant numbers of either of them. Without patent protection, drug companies will not get within a million miles of the gene. All that can be produced with non-patented genes are generic drugs, on which drug companies do not make money. You can argue they make too much money, but there is a reason that the US is at the forefront of the medical world, and money is a pretty good explanation. I do beleive selfish motivation produces the drugs, as that produces the money, and gets you the recognition. This is not like a software problem, where it will be solved by next year. Each gene WILL take years and millions of $, and with a failure rate (defined as not usefull for making a drug out of) at around 80%, you need some protection for the ones that work or you will never make any money.
EST patents are still under question, with no defense of them being mounted, but I would agree that they suck. You have no function on them at all, so patents on them are wrong. For whole genes, function is a lot more clear (although real far from crystal clear).
On a related note: If you get govenment grants (majority of researchers in US) you are required to patent, or otherwise protect your work BY LAW. Failure to do so will get you, and your university, in trouble.
I would guess that Larry Elison will not fight this. As everyone else has mentioned, most of the larger database companies have this provision in their EULA, Oracle being no exception. If Larry fights and wins, well he hasn't done his company any big favors, as now he will have also invalidated his own companies ban as well. I would guess he would be quiet now, as he has made his point, the press has noticed, and he doesn't have to say anything more to keep this story alive. The last thing he probably wants is to have that clause of EULA's tested.
Then again, IANAL and maybe Larry Elison doesn't care.
Pretending that politics are dead is a bit like the situation with the legal system and the online world. Online world pretends 100's of years of legal system will evaportate, and is then very shocked when it doesn't. Yes, most people who are not lawyers don't understand it, but that doesn't make it irrelevant. My uncle is a judge, and when he hears the cry's that the legal system is dead or that it can't keep up with the online world, He laughs and makes a comment about foolish young people who will grow up and learn. I think the same is true of politics. I think humans are political. You may be disgusted with the current system, but you can't pretend it doesn't matter (you do drive on roads, use libraries, call the police/fire dept etc... for which government is CRITICAL). Further, I think that government and politics are in-seperable. The second you have a concentration of power is the same second that you will have people fighting for it ( I think power is neccesary to get anything done, for and example of this not working, look at Somalia right now- massive lack of regualtion, and many there want a govenment so they can get infrastructure).
I think the utopian veiw has always existed just 30 years out, and that it will always remain about that far away. Humans will probably always be human (barring massive genome changes)
They announced that it will ship in the beginning of next year, and that the beta would be late summer this year. So far they have hit the beta release date (it was LATE summer!) but they haven't had a chance to miss the final release date yet. I give them an odds on chance of hitting it, but we will see.
I don't neccesarily think this is so. More people would give your more editing, more oversite to make sure one person is not writing garbage, more orginization, and more mouths to feed. Many will say that linux documentation works this way, I would disagree. Consistent style and presentation goes a long way toward making the book usefull, understandable, and ultimatly marketable. More cooks spoil the brew (in writing, not Coding, although I could argue that is true as well).
You have to pay the $60 to find out.....
I can''t speak for your school, but at mine we do not own the work. The school does (PhD) thesis. I am in the process of writing as we speak (should not be reading this) and have to sighn the copyright assighnment sheet to turn the thesis into the library. It is similar to when we publish papers in refereed journals, we also lose that copyright.
I am in biology (molecular immunology), so your field/school may be differant (sounds like it is) but I would not say the blanket statement that all of these thesis's (?thesi?) are taken without permission.
And no matter what the marketing droids do, that will continue to be Linux's greatest strength.
and its biggest weakness.... Most people just want "it" to work, and are not that interested in this particular strength.
The other serious mistake the author makes is somehow equating Linux as a GUI, then the GUI is xfree86. Ironically, X Windows is one of the oldest GUI's in existance, and the author is trying to make the point that it is too "new" to be mature and compete.
I remain uncertain as to the link between age-consistancy-quality-and ease of use. He says nothing about it being too new. Gnome and KDE are too new. They are still playing catch up to windows and the Mac.
And yet it's one of the most popular OSS programs today. Not a very good example of OSS failing is it?
By this criteria Windows is the best program in the world, and Microsoft writes all the best software in the world.
This truely is misleading, anyone can take a project and branch off of it is they feel the maintainer is not doing a good job
True- please start distributing your Linux Kernal with all the modifications that Linus et al do not want. The good projects HAVE not had this done to them, and there does seem to be an overlap been a group controlling and quality software (kernal, apache)
That makes sense from an end-user point of view, and that is fine, but as far as i'm concerned, end-users can go nibble a knob-end.
You could not have made his point any better than this.